Wait, wait, wait... How would MoS benefit from being PG? The violence is toned down? Uh. And? That's what was wrong with the last (still PG-13) big-screen Supes. Aside from the airplane/shuttle rescue the large-scale action was nonexistent.
I am tired of hearing about Donner's Superman. We get it. It's a classic. Moving on.
"Dark" is way overused as a term.
Taking the movie seriously = Dark.
More themes to think about = Dark.
No wink, wink, nudge, nudge. You're watching a movie based on a comic book. = Dark

PG-13 rating wasn't even around in 1978, didn't come out until 1984. Most the movies and CBMs that were released back then, from Star Wars to Indiana Jones, ESPECIALLY Indiana Jones, would have been rated PG-13. The first Donner movie was adult for it's time and the first Act is very serious and still holds up pretty well but there's definitely some hokeyness to it. The fact that they say Sugar Honey Ice Tea in it would have definitely upped the rating to PG-13 back then due to language, in the first film I mean.

I see nothing wrong with PG-13. Superman is just as "PG-13" as Batman....or should be at least.